This dissertation describes the past and recent progress in proton exchange membranes (PEM) for fuel cells. In particular the synthesis and characterization of materials for advanced alternative PEM were studied with an emphasis on structure-property and structure-property-performance relationships. The focus has included firstly a one-step synthesis and characterization of 3,3'-disulfonated 4,4'-dichlorodiphenyl sulfone comonomer. The procedure developed is adaptable for industrial-scale commercialization efforts. Secondly, the synthesis of aromatic nitrile containing poly (arylene ether sulfone) random copolymers was demonstrated. Various levels of disulfonation allowed the membrane characteristics to be investigated as a function of the membrane ion exchange capacity. The results favorably compare with the current state-of-the-art (Nafion™), particularly for direct methanol systems (DMFC). Thirdly, the mechanically and thermooxidatively stable copolymer membranes were blended with heteropolyacids producing nanocomposites which have potential in higher temperature fuel cell applications. Lastly, the basic PEM parameters such as water uptake, proton conductivity, and methanol permeabilities were controlled and presented as tunable properties as a function of molecular structure. This was achieved by in-situ control of chemical composition. The direct methanol fuel cell performance (DMFC) was much better than Nafion™. Hydrophobic surface properties of the membranes were improved by partial fluorination which made the Nafion™ bonded electrodes more compatible with the partially fluorinated copolymer membranes. The influence of surface enrichment had two important roles in increasing both initial and long term performance tests. The surface fluorine provided lower contact resistance and lower water uptake. The former was important for the initial tests and the latter provides for better long term performances. A delamination failure mechanism was proposed for the hydrocarbon membrane electrode assemblies (MEA) due to the large difference between water uptake of the catalyst layer and membrane and this was verified by a reduction in high frequency resistance (HFR) for the partially fluorinated systems. This thesis has generated the structure-property and structure-property-performance relationships which will provide direction for the development of next generation (PEM) materials.